Effect Chromatin Remodeling Factor DDM1 On Gene Expression By Histone Methylation H3K4me3 And H3K27me3 In Arabidopsis

Epigenetics refers to heritable changes in gene expression without changing the sequence of DNA.As an important mechanism of epigenetics,histone modification is very important for gene regulation and genome stability.DDM1(DECREASED DNA METHYL ATION 1)is an important chromatin remodeling factor in plants.In Arabidopsis,DDM1 mutations cause a decrease in whole genome-wide methylation levels and histone modification changes,as well as changes in the structure of nucleosomes,leading to changes in the density of chromatin.Although the effects of DDM1 on DNA methylation level in Arabidopsis has been investigated intensively,there are few studies on how DDM1 affects histone modifications and thus gene expression.In this study,we identified the regions where the H3K4me3 and H3K27me3 were differentially enriched in the wild type and ddm1-10 mutant under Col-0 background by ChIP-seq analysis.To check the effects of chromatin remodeling on histone modifications,we also examined the relationship of differential enrichment regions of H3 with H3K4me3 and H3K27me3 respectively.At the same time,combined with transcriptome analysis and genome-wide methylation analysis,we screened out genes whose expression are exclusively affected by histone modifications.H3K4me3 or H3K27me3,rather than DNA methylation.Our results will be helpful to further reveal the mechanism that DDM1 affects gene expression in Arabidopsis thaliana through various epigenetic modifications.The conclusions of this study are as follows:1.The number of H3K4me3 and H3K27me3 enriched regions is increased at the genome-wide level after DDM1 is mutated in Arabidopsis thaliana.At the same time,the distribution pattern of H3K4me3 and H3K27me3 enriched regions on each chromosome in the wild-type and ddm1 mutants are similar,indicating that these two modifications have no preference for chromosomes.At the same time,most of these two modified enrichment regions fall on the promoter region and gene body.2.Through analysis of the H3,H3K4me3,H3K27me3 differential peaks by ChIP-seq,we found that H3K4me3 and H3K27me3 are increased at the genome-wide level after ddml mutation.3.Through the screening of the differential express genes between Col-0 and ddm1-10,we identified a total of 340 up-regulated genes and 38 down-regulated genes in ddm1-10.The up-regulated and down-regulated genes were subjected to GO function enrichment analysis.The up-regulated genes were enriched in the biological functions of stress and resistance such as chitin response,organic nitrogen compound response,ethylene response and so on.The down-regulated genes fail to GO function enrichment.4.By analyzing the regions of H3 changes and the regions of H3K4me3 and H3K27me3,we found that the chromatin remodeling caused by the ddm1 mutation was not the main factor that lead to the changes of H3K4me3 and H3K27me3.5.Most of the differences between H3K4me3 and H3K27me3 peak are annotated to the promoter region of the gene.By association analysis of the differential peaks region with the differentially expressed gene,and excluding the effect of DNA methylation.There are 57 genes enriched with up-regulated H3K4me3 and up-regulated expression,which GO enrichment term is highly similar to that of differentially expressed genes.This shows that the up-regulation of H3K4me3 enrichment in ddm1 mutation in Arabidopsis plays an extremely important role in the biological function of ddm1 mutants.